CDP-ribitol (YMDB00867)

Identification
YMDB IDYMDB00867
NameCDP-ribitol
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionCDP-ribitol, also known as CDP ribitol, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. CDP-ribitol is an extremely weak basic (essentially neutral) compound (based on its pKa). CDP-ribitol exists in both E. coli (prokaryote) and yeast (eukaryote).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • CDP 5-ester with D-ribitol
  • Cdp ribitol
  • CDP-L-ribitol
  • CDPribitol
  • Cytidine 5'-(trihydrogen diphosphate), P'-5-ester with D-ribitol
  • Cytidine diphosphate ribitol
  • Cytidine 5'-(trihydrogen diphosphoric acid), p'-5-ester with D-ribitol
  • Cytidine diphosphoric acid ribitol
CAS number3506-17-0
WeightAverage: 537.3069
Monoisotopic: 537.076090169
InChI KeyDPJKHFICSGCNIR-HRENORGGSA-N
InChIInChI=1S/C14H25N3O15P2/c15-9-1-2-17(14(24)16-9)13-12(23)11(22)8(31-13)5-30-34(27,28)32-33(25,26)29-4-7(20)10(21)6(19)3-18/h1-2,6-8,10-13,18-23H,3-5H2,(H,25,26)(H,27,28)(H2,15,16,24)/t6-,7+,8+,10-,11+,12+,13+/m0/s1
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[hydroxy({[(2R,3S,4S)-2,3,4,5-tetrahydroxypentyl]oxy})phosphoryl]oxy})phosphinic acid
Traditional IUPAC Namecdp ribitol
Chemical FormulaC14H25N3O15P2
SMILES[H][C@](O)(CO)[C@]([H])(O)[C@]([H])(O)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose-5-phosphate
  • Pentose phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Polyol
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Primary amine
  • Primary alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility15.9 g/LALOGPS
logP-1.7ALOGPS
logP-5.5ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area291.59 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity104.95 m³·mol⁻¹ChemAxon
Polarizability44.37 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG Pathways
Pentose and glucuronate interconversionsec00040 Map00040
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900010000-6e1fcdeba40ba224ed0bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3910000000-ae705be2942ba94101e1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-6910000000-f3aaafb52fa945f1a801JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01w0-9401840000-00c2c44a62fdbcf52c04JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-08fr-9533100000-b72dd29a8a03e4ce91e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0bvl-6910000000-04014d88bb0d69f9f1c7JSpectraViewer
References
References:
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • SHAW, D. R. (1962). "Pyrophosphorolysis and enzymic synthesis of cytidine diphosphate glycerol and cytidine diphosphate ribitol." Biochem J 82:297-312.13911452
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16022
HMDB IDNot Available
Pubchem Compound ID46878411
Kegg IDC00789
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available